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Human menin with bound inhibitor MIV-3S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GPQ pdb entry 4GPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 283 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.915 α = 90 b = 80.207 β = 90 c = 124.659 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 300 mm CCD 2011-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0331 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.45 38.48 100 0.087 36.5 7.3 633852 87254
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 4GPQ 1.45 38.48 82790 4372 99.86 0.16295 0.16158 0.1635 0.18856 0.1898 RANDOM 25.065
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.59 0.37 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.76 r_dihedral_angle_4_deg 16.975 r_dihedral_angle_3_deg 11.716 r_long_range_B_refined 9.04 r_long_range_B_other 9.04 r_scangle_other 6.251 r_dihedral_angle_1_deg 5.828 r_scbond_it 5.154 r_scbond_other 5.153 r_mcangle_it 3.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.76 r_dihedral_angle_4_deg 16.975 r_dihedral_angle_3_deg 11.716 r_long_range_B_refined 9.04 r_long_range_B_other 9.04 r_scangle_other 6.251 r_dihedral_angle_1_deg 5.828 r_scbond_it 5.154 r_scbond_other 5.153 r_mcangle_it 3.356 r_mcangle_other 3.356 r_mcbond_it 2.642 r_mcbond_other 2.642 r_angle_refined_deg 1.996 r_angle_other_deg 1.178 r_chiral_restr 0.211 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3686 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 92
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling